def updateAnnotation(rosrs, rouri, resuri, bodypath, bodycontent):
bodyuri = getResourceUri(rouri, bodypath)
log.info("UpdateAnnotation:")
log.info("-- resuri: %s"%(resuri))
log.info("-- rouri: %s"%(rouri))
log.info("-- bodyuri: %s"%(bodyuri))
# If annotation is not aggregated in RO, add it
(status, reason, headers, uri, data) = rosrs.getROResource(bodyuri, rouri)
log.debug("Get annotation %s: %03d %s"%(bodyuri, status, reason))
if status == 404:
(status, reason, proxyuri, newbodyuri) = rosrs.aggregateResourceInt(
rouri, bodypath, ctype="application/RDF+XML", body=ANNOTATION_EMPTY)
assert status == 201, "Aggregating annotation body %s - status %03d %s"%(bodyuri, status, reason)
assert newbodyuri == bodyuri, (
"Aggregated annotation URI mismatch %s (expected %s)"%(newbodyuri, bodyuri))
log.info("-- Created empty annotation body (%s)"%(bodyuri))
# If annotation stub does not exist, create new
bodyuris = list(rosrs.getROAnnotationBodyUris(rouri, resuri))
log.debug("--- bodyuris:\n"+"\n".join([repr(u) for u in bodyuris]))
if not bodyuri in bodyuris:
(status, reason, annuri) = rosrs.createROAnnotationExt(rouri, resuri, bodyuri)
assert status == 201, "Creating annotation stub for %s - status %03d %s"%(bodyuri, status, reason)
log.info("-- Created annotation stub for resource (%s) with body (%s)"%(resuri, bodyuri))
# Replace annotation body
(status, reason, headers, data) = rosrs.doRequest(bodyuri,
method="PUT", ctype="application/RDF+XML", body=bodycontent)
assert status in [200,201], "Updating annotation body %s - status %03d %s"%(bodyuri, status, reason)
log.info("-- Updated annotation body (%s)"%(bodyuri))
return
<roterms:resource rdf:resource="&BUNDLE;workflow/Create_SNP_Set/in/Entrez_ID" />
</rdf:Description>
</roterms:inputValue>
<roterms:inputValue>
<rdf:Description>
<roterms:portName>set_width</roterms:portName>
<roterms:resource rdf:resource="&BUNDLE;workflow/Create_SNP_Set/in/set_width" />
</rdf:Description>
</roterms:inputValue>
<roterms:inputValue>
<rdf:Description>
<roterms:portName>path_to_output_file</roterms:portName>
<roterms:resource rdf:resource="&BUNDLE;workflow/Create_SNP_Set/in/path_to_output_file" />
</rdf:Description>
</roterms:inputValue>
</rdf:Description>
</rdf:RDF>
"""
# Main program script
if __name__ == "__main__":
# Set up ROSRS session and key values
rosrs = ROSRS_Session(ROSRS_API_URI, accesskey=ROSRS_ACCESS_TOKEN)
rouri = getResourceUri(ROSRS_API_URI, RO_PATH)
resuri = getResourceUri(rouri, RES_PATH)
# Add annotation
updateAnnotation(rosrs, rouri, resuri, ANNOTATION_PATH, ANNOTATION_BODY)
# Finish up
rosrs.close()
